BLASTPAT and FASTPAT Pattern Database Search Tools for
Fast and Sensitive Gene Function Identification
BLASTPAT and FASTPAT are tools designed to identify protein sequences
whose functions are not identified by standard BLAST or FASTA database
searches. These modified versions of BLAST and FASTA perform rapid and
sensitive searches of our Pattern Induced Multiple Alignment (PIMA)
Pattern Database. The PIMA Pattern Database contains 22,422 patterns
generated from multiple sequence alignments of 12,669 protein families
we have identified in the NCBI's Entrez protein sequence database.
Both FASTPAT and BLASTPAT searches can be performed using the BCM
Search Launcher WWW pages, provided by the Human Genome Center, Baylor
College of Medicine (Houston, Texas):
http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html
Patterns in the PIMA database are encoded by a maximized information
content alphabet. This extended alphabet includes the standard 20
letter IUPAC amino acid codes plus 61 other characters (lowercase
characters, digits, other symbols) representing those combinations of
residues which contribute the highest information as observed across
all aligned positions in our protein family alignments.
Pattern database searches are performed using new log-odds scoring
matrices that we have developed for use with this new extended
alphabet. In contrast to standard scoring matrices like PAM or BLOSUM,
these new pattern-based matrices distinguish between conserved and
variable positions, increasing search sensitivity and selectivity.
A more detailed description of these program is available on our WWW pages:
http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/blastpat.htmlhttp://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/fastpat.html
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Istvan Ladunga, Brent Wiese, and Randall F. Smith
Human Genome Center, Department of Molecular and Human Genetics and
W.M. Keck Center for Computational Biology
Baylor College of Medicine, Houston, TX 77030, USA
{istvanl,brent,rsmith}@bcm.tmc.edu; 713-798-8089, FAX: 713-798-5386
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